BACKGROUND: Research on physical activity breaks and facilities (indoor and outdoor) in secondary schools is relatively limited. METHODS: School administrators and students in nationally representative samples of 8th (middle school) and 10th/12th grade (high school) students were surveyed annually from 2008-2009 to 2011-2012. School administrators reported information about physical activity breaks and facilities. Students self-reported height, weight, and physical activity. RESULTS: The prevalence of physical activity breaks and indoor and outdoor facilities (dichotomized by median split) differed significantly by region of the country, school size, student race/ethnicity, and school socioeconomic status (SES). Breaks were associated with lower odds of overweight (adjusted odds ratio [AOR] = 0.91, 95% confidence interval [CI]: 0.83-1.00) and obesity (AOR = 0.86, 95% CI: 0.75-0.99) among middle school students. Among low-SES middle school students and schools, higher indoor facilities were associated with lower rates of overweight and obesity. Among high school students, higher indoor and outdoor facilities were associated with 19-42% higher odds of moderate-to-vigorous physical activity. CONCLUSIONS: Physical activity breaks and school facilities may help to address high rates of overweight/obesity and low physical activity levels among secondary students, especially lower-SES students. Students in all schools should have equal access to these resources.